The irrepressible and ingenious Dana Sterling leads her squad in a practice drill while the Southern Cross goes from red to yellow alert. The green troop runs afou]l of seasoned combat veterans led by Lieutenant Marie Crystal. The verbal battle dissolves into physical conflict and, after leading the military police patrol, led by Marino, on a wild chase through Monument City, Dana finds herself thrown in the brig to reconsider her behavior in solitary confinement. Later, Dana is berated by Colonel Alan Fredericks. She has failed to exercise conduct becoming either an officer and daughter of two well-loved war heroes. The young woman begs for another chance. Fredericks agrees to give her one more opportunity to prove herself. Dana is soon released in time to lead her squad into their first official combat.

Because of her splendid efforts against enemy forces, Dana is directed to take command of the 15th Alpha Tactical Armored Corps. Their previous commander, Captain Sean Phillips, is demoted to private second class for yet another of many indiscretions – this particular one involving a colonel’s daughter. Sean takes the setback in good-natured stride. Meanwhile, Dana is troubled by visions of an alien being she had seen during combat.

Citizens of Earth are advised by Macross Broadcasting System that war has been declared with the Robotech Masters. Military discipline becomes the order of the day. Sterling’s 15th ATAC Squad is ordered to take position as rear guard defense. Civil Defense is too tame a position compared to what the young lieutenant has in mind for an active military career but she carries out her orders – until she sees main base going up in flames. Mobilizing existing troops, Sterling returns to the base and attacks the invading bioroids. In the heat of battle, one particular unit catches Sterling's attention - a red bioroid. Due to 15th Squadron's quick actions, they repel the invading force, and Dana is promoted to 1st Lieutenant.

In the course of the battle to regain the post, Dana sees the red bioroid that has been the focus of her disturbing visions. It is an unusual mecha, but Marie and Dana manage to defeat it and rout the invaders from the space station. Soon, communications between United Earth Command Headquarters and Space Station Liberty are reestablished.

Military Intelligence eventually confirms that the aliens are digging at the ruins of the old SDF-1. They are mystified as to what the Robotech Masters could possibly want or salvage from the old wreck, beside Earth's dwindling supply of Protoculture. Their meeting is interrupted by a large-scale bioroid attack.

Bowie Grant, member of the 15th Squad and was captured after wandering too near the area, is convinced the Robotech Masters mean to kill him, Bowie wastes no time discovering a means to escape confinement. He breaks out of his cell and finds a way outside as the 15th Squadron engages the enemy. Once again, Dana finds herself face to face with the red bioroid pilot. This time, both experience an unsettling moment of recognition.

Reinforcements arrive to help the 15th rescue Bowie. The Robotech Masters’ huge advance command ship retreats, rising slowly into the air carrying not only the compliment of bioroids but their strange commander as well.

Since neither side is willing to make even the smallest concession, the war between Earth and the Robotech Masters escalates into another serious military confrontation. Supreme Commander Anatole Eli Leonard, under orders from the civilian Prime Minister Moran, deploys the bulk of their Tactical Armored Space Corps to engage the enemy in space in an attempt to avoid turning the planet surface into a battleground, but the strategy is based on insufficient data. Most of the troops are wiped out while the survivors are left to drift helplessly in space. On the hasty decision of a few stubborn men, hundreds of lives have been lost in a single hopeless gesture. The Robotech Fortress continues to orbit Earth, untouched, unscathed, and apparently unbeatable.

Professor Miles Cochrane and his colleague, Dr. Samson Beckett, examine trace remains of a downed bioroid pilot and make a disturbing discovery. Their analysis of the alien’s genetic code determines that the invaders are possibly human – not micronizedZentraedi as they had originally suspected. They are horrified at the thought of brother fighting brother.

Dana Sterling volunteers the 15th Squad to rescue the space corps. Louie Nichols has determined that the alien ship twists opposing forces in a series of hyper folds to move from place to place. Dana devised a plan to upset the hyper-balance of the alien craft. While everyone agrees that the plan could work, they run into difficulty with Chief of Staff Rolf Emerson, Bowie Grant’s guardian. After the recent disaster, Emerson does not want to risk his ward’s life in another futile military maneuver. Bowie, Dana, and Louie convince Emerson to see their point of view.

The 15th Squad not only rescue their fellow defenders, they disable the alien mothership. What was once an invincible source of terror crashes to the planet’s surface, a fiery symbol of mankind’s first victory.

Supreme Commander Leonard wastes no time in sending Dana Sterling and 15th Squad into the alien ship. Helmet monitors transmit their findings to Central Command. However, as they scout the ship’s interior, the Robotech Masters are making their own observations in return.

The team discovers a bio-mechanical operation that indicates the aliens are able to create perfect androids. Separated from the group, Bowie meets a beautiful alien woman, Musica, the mistress of the Cosmic Harp. Musica manipulates the electronic beams of the fantastic instrument. However, the two are attracted to each other by more than their love of music. Bowie is enchanted, but Musica finds her own reactions too disturbing; they go against all her conditioning. After she helps Bowie to defeat attacking sentries, she runs away.

Meanwhile, the Robotech Masters trap Dana and her crew. Sterling blasts her way out through the floor. Guessing their welcome is over, the squad heads for an exit – any exit! On their way out, Sterling captures an enemy bioroid.

An analysis of the 15th Squad’s observations supports Command Central’s theory that the Robotech Masters have come to Earth in search of the last known protoculture matrix. A preliminary report on the captured bioroid indicates the bio-mechanical weapons are controlled by programmed androids. The bioroids cannot be stopped unless the cockpit controls are destroyed. Dana violently objects, claiming that blasting the cockpit would kill the pilot. Supreme Commander Leonard seems to find this information especially satisfying and announces: "Gentlemen – it seems to me our course is clear. We must commit ourselves to the destruction of these androids whenever they appear. You don’t believe we could ever come to terms with a group of barbarians like them? Their advanced technology leaves us no choice. Even if we could negotiate, we’d be doing it from a position of weakness, not strength, and that would be fatal. It’s out of the question."

Although Dana suspects Leonard’s orders evolve from fear and prejudice, there is no way she can successfully contradict him. She is concerned that not all the bioroid pilots are mechanical androids but actual living sentient beings, capable of emotions – like her mother. The lieutenant leaves the conference feeling very disturbed.

The Robotech Masters are in a perplexing situation. The secrets of protoculture production have been lost with the passing of their creator, Zor. All attempts to rediscover those secrets through the cloning of Zor have ended in failure. Confrontation is their final alternative. The true threat to Earth and the protoculture matrix derives from the approach of another alien race, the parasitic Invid. The Elders are desperate to recapture the matrix before their civilization collapses around them, but too many of their bioroid pilots have been injured in battle to mount an effective attack. The Robotech Masters decide to capture human beings to determine if they can be reprogrammed to pilot bioroids.

Alien troops capture more than 200 civilian hostages. Leonard has them listed as casualties of war despite the protest of Rolf Emerson.

At Command Central, Dana Sterling tries to stop Leonard from killing a captured alien pilot. Although she knows her actions place her career in extreme jeopardy, she cannot stop herself from protesting an action she instinctively feels is wrong. Dana can’t believe the enemy troops are unthinking androids. Her continued attraction to the red Bioroid pilot makes this theory particularly upsetting.

Dana is reduced to seeking solace at a bar. Bowie Grant accompanies his commander. Sterling meets an interesting entertainer, George Sullivan. Hoping she’s found the answer to her romantic dilemma, Dana slips backstage for further conversation only to discover that the man is an agent for the Global Military Police. He convinces her to help him and she agrees. However, the mission goes awry and Sullivan is killed.

Major John Carpenter's ship arrives near earth after nearly 15 years in deep space.

The mysterious red bioroid pilot is captured, and Dana Sterling finds her problems are just beginning. The more she tries to dismiss the mysterious warrior, the more compelling he becomes. She has no way of knowing he is Zor Prime. A clone of Zor, the genius who created the science of Robotech – and, inadvertently, Earth’s continuing conflict with invading alien forces. Long ago, the first Zor escaped with the secrets of Robotechnology on the SDF-1 to prevent their abuse by the Robotech Masters. Now, the Robotech Masters seek to manipulate Zor Prime in ways they could never control the original. With a neuro-sensor implanted in his body, the clone will serve as an unknowing spy for the alien invaders.
Later, Tokugawa-class Battlecruiser Recon-1 arrives from the Pioneer Mission. The ship is destroyed as they force themselves through the Robotech Master's blockade, and the survivors land near the outskirts of Monument City. Dana Sterling and Sean Phillips arrive to pick up Major John Carpenter and his aide who were part of the Robotech Relief Expedition. They are taken to United Earth Command for debriefing. Leonard is staggered to hear there will be no reinforcement arriving from the Robotech Expeditionary Forces. It would seem Earth’s survival rests on strategic information gathered from the mysterious alien pilot.

Dana Sterling's exercise regimen is interrupted by an emergency call from General Emerson's office. When she arrives, she is given a new assignment: the alien Bioroid pilot, Zor (not named Zor Prime as earth forces didn't know that designation), needs to be debriefed, but his memory is completely wiped out. General Emerson puts him under Dana's personal direction. It is his hope that exposing Zor to a military environment will jog his memory somehow.

Dana chooses an amusement park as the setting for her “debriefing” session with Zor. She does little to contain her enthusiasm at spending some time having fun with the strangely compelling alien, but a trip on the space tunnel ride not only starts to unlock memories within Zor, but almost proves fatal for Dana when her harness breaks.

The next day, Zor goes over images of the Robotech Masters' ships and weaponry in the hope that it will jog his memory. However, an image of the mounds that cover the ruins of the SDF-1 sets off voices in his mind: “Earth is the final source of Protoculture, the basis for our power, the lifeblood of our existence. Our foremost goal is to control this life force by conquering Earth.” Zor collapses and starts muttering fragments of what he's heard. The Robotech Masters analyze the images Zor's neurosensor has provided them. They are worried about Zor's returning memories, even more so about whatever it is Zor Prime has recognized in Dana. His emotions relating to her may be the key in his memories returning. For this reason the Masters decide to start controlling Zor Prime directly.

In a staff meeting, Supreme Commander Leonard relays what has been learned from Zor to the rest of the Southern Cross command. Emerson feels that since they know what the Robotech Masters are after, they should try negotiating with them, but Leonard decides that now is the time to attack.

In the exercise room, Zor mulls over his supposed humanity. In search of those answers, Zor goes to General Emerson's office, but stands outside when he hears people talking inside. Emerson and Colonel Rochelle are discussing Commander Leonard's reckless new plan of attack. Angelo Dante, member of the 15th, notices Zor walking away from Emerson's office and grows suspicious. Above the Earth, the Masters are pleased with Zor's performance. ”One simple fate remains for the Micronians,” one among them states, “that we will annihilate every one of them.”

At headquarters, Supreme Commander Leonard addresses a room full of Southern Cross officers. "We fully realize there has been much debate over the advisability of a preemptive strike against the alien fleet at this juncture," he tells them. "These concerns have been taken into careful consideration by the high command of the armed forces. But now the time has come for putting an end to debate and for uniting all our forces behind a common effort." He goes on to explain that the new Armored-Gyro Assault Choppers (AGACs) will form the nucleus of the first assault wave. Not everyone is convinced of this plan.

Soon, the “Ajax” choppers are being loaded into Tristar, Nelson and Ardennes-class starships in preparation for the attack. As TASC personnel rush to their ships, Sean pays Marie a quick visit to say goodbye. He tells her to be careful. "I almost believe you really mean that," she retorts with a smile before heading to her ship.

Zor Prime watches the ships as they prepare to lift off, and through his eyes the Masters watch as well. While one among the three Robotech Masters triumvirate points out that this is the largest fleet they have amassed against them, another assures his companions that, "the more ships they employ, the greater our triumph!" Soon, the transmission breaks off.

Zor and Dana Sterling viewing the lift-off.

At that moment, Angelo asks Zor what he's doing in an off-limits sector. Zor claims he just wanted to watch the liftoff. Dana soon arrives to tell Angelo it's all right. As Zor and Dana look on, the fleet takes off. Others watch as well, including a proud Supreme Commander Leonard and the similarly boastful Robotech Masters. Aboard the ships, men and women rush to battle stations as the fleet nears the Masters' motherships. Marie tells her men it's time to take out the AGACs, but as the battle begins none are deployed. Instead, the fleet fire their cannons at the Masters' flagship. The Masters retaliate, blasting two Southern Cross ships to atoms within a few moments.

Back on Earth, Dana and Zor have left the city for a grassy field that Dana says reminds her of where she grew up. She says she always starts thinking about her hometown when she comes up here and the people she left behind. Zor says he'll never be able to go home again. "A man without a past is a man without a home," he tells her. She reminds him that his memories are coming back, and Zor goes back to that attack he vaguely remembered. He wishes he could remember where and why that attack took place. Something suddenly occurs to Dana, and she leads Zor away.

In space, another Southern Cross battlecruiser is destroyed. Captain Nordoff informs Leonard that a third of the fleet is gone along with half of their transports. He suggests withdrawing, but Leonard asks why the AGACs haven't been deployed. Nordoff doesn't think they have a chance when the Masters' ships have been wiping out their largest battlecruisers with ease, but Leonard remains stubbornly insistant that the AGACs be dispatched immediately. Nordoff scrambles the AGACs. To counter the incoming ship, the Masters deploy a large force of their assault carriers.

Dana, Bowie, and Zor arrive at the mounds that mark the site of the SDF-1's destruction. Zor finds something familiar about the spot, but he tells them it looks very different. The three decide to look around. Dana spots an opening, and the three enter with Zor in the lead. A ray of light leads them into a large chamber in which they find a number of strange plants. When Dana reaches out to touch one, it strikes her. Zor points out that they're growing in threes--the three who act as one, the same as his dream. Bowie asks if these plants might be what the aliens want to get their hands on, but Zor doesn't know. The mobilization of a second assault wave, which is to rendezvous with the operational units from the first to prepare for a combined attack against the Robotech Masters. "And this time," he proclaims, "we'll fight to the very last man!"

Leonard’s desperate frontal assault proves to be a disaster. The shattered Earth fleet withdraws toward the dark side of the moon, but the Robotech Masters aren’t celebrating yet. Transmissions from Zor Prime alert them that the "Invid Flowers of Life" growing within the ruins of the SDF-1 are in full bloom. It marks the first signal of the approaching Invid invasion force. The Robotech Masters’ biosynergetic reservoirs of protoculture are running dry. Weapons and defense systems are a constant drain, consuming more energy than they create. If the Robotech Masters cannot secure an infusion of fresh protoculture, their civilization will come to an end.

Musica and her sisters, Allegra and Octavia, are approached by potential mates Karno and his triumvirate brothers, selected for them by the Robotech Intelligence Triumvirate. Tormented by strange new emotions after her encounter with Bowie Grant, Musica refuses to obey the Robotech Masters. Her behavior does not go unnoticed. Like the Zentraedi, Micronian culture has an unsettling effect on the clones. The mistress of the Cosmic Harp has become as unpredictable as Zor Prime.

Elsewhere, Air Cavalry One relief forces led by Lieutenant Marie Crystal succeed in rescuing Leonard’s decimated Earth fleet. On her return to the planet, she finds Sean Phillips waiting for her. It would seem that her military and romantic strategies have paid off.

Supreme Commander Leonard then places his arch-rival, General Rolf Emerson, in command of a second offensive against the enemy. Despite conjecture to the contrary, Emerson rejects speculation that he is piloting a suicide squad. According to Dennis Brown, leader of the Black Lions Squadron, all the officers appointed to the mission are those who consistently oppose Leonard’s decisions, and the odds for success are very much against them this time. Still, Emerson is determined to return victorious.

Marie and Sean’s important date becomes a disaster. The lieutenant finds Sean apparently involved with a girl from his past. Marie runs away. Sean tries to explain, but she departs with Emerson’s fleet before he gets the chance.

The Robotech Masters take note of the arrival of an Invid Sensor Nebulae, a gaseous cloud that scans the universe in search of significant Protoculture signatures. They fear the Invid will soon arrive to reclaim their Flower of Life. The Sensor Nebulae lingers as it acts as the Invid's eyes and ears of the escalating conflict on Earth.

The ships under Rolf Emerson's command draw ever closer to the Masters' fleet. Aboard General Emerson's ship, the general orders his ships to standby in first alert position. The lunar-bound fleet is moved to second alert position. It enters the outer fringe of the nebulae, and the Masters' flagship comes on-screen. Emerson asks if they seem to be readying an attack, but an officer reports back a negative. Rochelle suggests a surprise attack, but Emerson says their first and foremost goal is to orbit Luna. As they clear the nebulae, he orders the fleet to move to third alert position, but to keep their eyes on the Masters' ship.

Inside the ship, the Masters are informed that the Southern Cross ships have passed nebulae area 21. "They must be relieved to have passed our zone without confrontation," one boasts. "Prepare to destroy them." Soon, the Masters have surrounded the fleet. A bridge officer warns Emerson that their ship won't be able to hold out much longer. Colonel "Ace" Green tells him they need reinforcements, but Emerson says that's impossible--their ship is the only one capable of sustaining this orbit. After checking their orbit time and orbital location, the general determines that they may be able to create a phenomenon known as the molecular vacuum. "I've heard of that, General," Green says. "That's where space within a radius of two kilometers can be warped." Emerson asks what happens to objects in that space. "They'd almost certainly break up into atoms and be sucked into a small black hole on a one-way trip into another dimension." Green is appalled, but Emerson tells all forces to lead the Bioroids within two kilometers of his flagship before 2300 hours. Green warns him that they may be sucked in as well, but Emerson thinks there's no other way to survive. The countdown begins.

Emerson tells the fleet to ready weapons but not to start firing. Despite only a twenty percent chance of breaking through the barricade, Emerson decides to give it a try. Bioroids are launched to counter their escape, and AGACs are launched in retaliation. With just over eighty-eight percent of the Bioroids in position and three minutes until the Molecular Warp Blast, Emerson orders his ships to clear the flux area as soon as possible. Energy surges around the flagship, and it begins to glow red. Light radiates from it, and the nearby Bioroids begin to explode. Soon, all that's left is debris. Marie assures her pilots that the flagship will be back, but in the meantime they come under fire from a pair of surviving enemy ships. She is surprised when a flash of light appears behind them that causes the ships to explode. The flash turns out to be General Emerson's flagship, reemerging from the warp.

Back on Earth, Louie, after tinkering with special glasses connected to an arcade machine, beats the all-time high score. Dana is impressed. "It's as if theres a machine gun built right into your glasses!" she exclaims. "Exactly," Louie explains. "The glasses pick up the movements of my pupils and respond with impulses which program the memory in the cartridge. The cartridge remembers the patterns on my pupils, producing a recognizable firing zone, which is activated by organic impulses produced when my pupils intercept the reflected light from the target." He calls it Nichols's Special Vision Track Firing System (VTFS), or the Pupil Pistol. A couple of officers from the Robotech Department, clad in yellow come by to examine the system. "This could be useful in the plan," one cryptically notes. The other, Major Cromwell, tells Dana and Louie that they will lend their assistance and equipment to the upgrading of this system. Cromwell says the device will play a crucial role in their simulation training. But in Supreme Commander Leonard's office, it is revealed that the equipment is being mass-produced for use in the next offensive.

The best genetic stock of the Robotech Masters are used to pilot the new Bioroid Invid Fighter.

Transport Squadron 85 arrive from hyperspace, reinforcements responding to a mayday from the first attack on Space Station Liberty. The ships of Transport Squadron 85 arrive at Moon Base ALICE, and are welcomed back by General Emerson, who tells them they've been called back from deep space to aid in a plan they hope will bring the war around. They are to go into Earth orbit, where he will join them to lead them into battle. The ships take off from their underground hangars, and depart for Earth.

The Masters continue to watch the humans prepare with keen interest. One of them asks the Scientist Triumvirate if the humans are preparing anything against the Invid and their Sensor Nebulae, but all the humans seem to be preparing is a large offensive against them.

Finally, all personnel are ordered to their transports. Dennis Brown and Nova Satori each tell each other to take care before Lt. Brown gets to his transport. The ships lift off. The Southern Cross warships begin their operation. They fire all their weapons at the Masters' flagships. As heavy as their fire may be, aboard Emerson's flagship Green notes that the Masters' ship isn't taking much damage. Emerson thinks maybe they're using a type of energy shield they haven't seen before. He orders them to press the attack. A heavy missile barrage finally cracks the hull of the Masters' ship, and the 15th Squadron is launched to take advantage of the opening. The space borne Hovertanks lower themselves to the surface of the flagship, and Dana asks where the Bioroids are. Angelo doesn't like it. Indeed he shouldn't, as the Masters decide now is the time to test out their Invid Fighters.

Inside the Invid Fighter hangar, the guard triumvirates, collectively known as Vada Prime, assume command of their mecha. "Three will always be as one!" they are reminded. "One for three and three for one, in thought and action and in reaction!" Their mission is to defend all weak points and destroy all human life. They are assured victory.

General Emerson decides they need to make the opening bigger, and Green suggests ramming the Masters' ship. Emerson approves the idea. Despite the onslaught of enemy blasts, the ship continues towards the Masters' flagship. The 15th is ordered to clear the area as Emerson's ship skids across the hull of the enemy ship, widening the hull breach. As the 15th prepares to enter the enemy ship, Emerson's flagship comes under heavy attack. Green suggests immediate withdrawal. Despite his own personal objections, Emerson orders all forces to withdraw, except the 15th.

Inside the Masters' ship, the Robotech Masters realize that the invading 15th has discovered the Invid Fighters' weakness. They decide to reactivate Zor Prime. Within the corridors of the enemy ship, the reactivated Zor flees. Dana calls out to Zor, and is soon accompanied by Angelo, who switches to Guardian mode and starts blasting pillars to try to lure Zor out. Dana does the same, blasting open a door. Behind the flames is a familiar sight--a red Bioroid. The Bioroid cockpit opens, and from it emerges Zor Prime. "You have fallen into this trap much more easily than I would have ever expected, Lieutenant Sterling," he says mockingly. They are now his prisoners, and any attempt to escape will mean the 15th Squadron's certain doom. "You and the entire 15th Squadron," he boasts, "are powerless against the Robotech Masters!"

The Robotech Masters notice a deviance in Zor's brain wave pattern. Their scientists suggest that his exposure to the humans has produced an adverse affect on his anterior brain cells. One Master asks if they are suggesting an awakening of a dormant racial memory, and indeed they are. The Masters agree that the deviance must be eradicated.

Once the group shake off Zor and are reunited, Angelo ponders their next move. Dana suggests finding the ship's command center or bridge, then taking it by force.

In another corner of the ship, as Musica plays her Cosmic Harp, her sisters arrive to inform her that a group of alien soldiers has invaded the central corridors. She asks if any have been captured. Karno, she is told, has started an all-out search. Despite warnings, Musica decides to leave. She needs to be alone.

Dana, Bowie and Louie somehow end up getting cut off from the rest of the 15th Squad. A series of bizarre experiences leads Dana to getting separated from her two companions. At the bottom of an escape chute, she lands on and bounces off of a pale green-haired clone before landing on the floor. The clone, named Latell, awakens and asks where she came from. "You wouldn't believe it," she tells him, wincing in pain. He asks her if she's hurt and if there's anything he can do to help. Dana asks where she is. "Why, this is the district interim center for purging and replacement," he says. She wonders what they're purging. "Why, the personal consciousness of those whose original bodies are being rehabilitated." Dana asks how, and Latell is amazed that she doesn't know. She quickly adds that she just doesn't remember. He gets ready to explain before being told by a supervisor that his rest period is terminated and his training is to resume. The supervisor tells Dana to go as well, and Latell leads her away.

Dana and Latell eventually arrive in a room filled with bodies in liquid-filled tanks. She asks what they are, and then notices a body that looks just like himself. He tells her this is his physical body. It is still alive, but in a state of suspended animation. It will remain here until its cells are completely purged of individual thought. At that word, a trio of guards arrive, intent on seizing their prey no matter the cost. They blast his body free of its suspension tank, killing it. Enraged, Dana leaps at them, kicking one in the face and punching another out. The third she chops in the back of the neck, but as Latell leads her into another room, another pair of guards arrives. The clone hands her a proto-transmitter that will lead her to the main control center so that she can destroy it. He tells her he'll stay here while she goes. He stands to surrender while Dana starts to sneak off, but she soon goes into a run. The guards aim and fire, hitting the intervening Latell instead of their target. Dana stops and goes back for him, outraged that they shot one of their own. "Please do not feel badly," Latell tells her. "You are freedom, and my life means nothing."

That leaves Sean and Angelo, who somehow managed to get pinned down in a corridor, horribly outmanned and outgunned. They keep firing in hopes of going forward, until Sean looks back and notices what Angelo doesn't--that they can't go back, either. They're surrounded.

Angelo and Sean are taken to a holding cell where they're once again reunited with their comrades--Bowie, Louie, and Dana have been caught as well.

Once again, Musica plays the Cosmic Harp, and once again she is troubled by emotions. She devises a desperate plan and leaves her sisters in shock.

At that moment, a tired and confused-looking Zor Prime wanders through the ship's residential sector. A veiled Musica yanks him out of the wayin time. He falls over, and Musica looks up to see a trio of guards accompanied by the three Clone Masters. Karno and his brothers arrive behind her. "Zor Prime is no longer a dependable clone, and therefore must be dealt with accordingly." Karno is ordered to prepare Zor for deprogramming, after which he and the humans will be destroyed. As Karno's triumvirate carries Zor Prime away, Musica tries to plead with him, but he reminds her that she refused him when they were to be mates so he has no reason to disobey orders for the likes of her. With the guards and Clone Masters gone, Musica is alone for only a moment when her sisters arrive to try and comfort her. She slaps Octavia's hand away, asking to be left alone, only to soon realize the gravity of what she has just done. Telling them she must find Bowie, she runs away. The two clone sisters fear that they have truly lost Musica.

Outside, Musica asks forgiveness from her people as she starts up a hovercraft and jumps from it as it careens towards a pair of guards leading the 15th Squadron away. Musica leads them to what Louie acutely identifies as the nerve center of the ship. They find Zor Prime about to have his memory erased. The members of the 15th ATAC leap down from the smashed window and Dana tells everyone not to move. They then make their daring escape from the mothership. Sure enough, Louie manages to jury-rig five Bioroid skysleds, manned now by the Battloid mode Hovertanks of the 15th Squadron. They escape into space as the mothership begins to explode around them.

Outside the ship, AGACs and Bioroids clash. From his flagship, General Emerson orders all AGAC pilots to maintain battle formation and orders the second wave to launch on his order.

Within the mothership, the last Invid Fighter falls before Zor Prime's Red Bioroid. "I betrayed my friends, and now the only to redeem myself is by betraying my people! Everything I touch turns to ashes! So be it!" He raises his blaster one more time. "Goodbye, Dana!" he says to himself as he pulls the trigger, firing his blaster at the central core of the flagship. To Dana's relief, Zor Prime survives as he escapes the explosion of the mothership.

Meanwhile, a small fleet of transport vessels departs from the exploding mothership. On-board one of them, Allegra and Octavia lament their separation from their sister. And in the cockpit of Bowie's Hovertank, Musica is feeling the same way, even though she tells Bowie nothing is wrong. The two watch as the Robotech Masters' mothership is completely destroyed. She bids her sisters farewell.

The remnants of Emerson’s force withdraws toward Moon Base ALICE as a shuttle bearing the 15th Squad, Zor and Musica return to Earth. The peace they find there is short lived as the Robotech Masters call full-scale assault on Earth. Nearly 70 percent of their remaining protoculture pods have been invaded by the Invid Flower of Life. The infected mass has degenerated to the point where it is no longer of any use to them. They are concerned that the Protoculture Factory on Earth has been similarly contaminated. They must retrieve what they can before the Invid arrive.

At Command Central, Leonard decides to join Emerson and launch a final offensive: "we will knock them out of the skies or die in the attempt." His fellow officers agree.

Bowie and Musica hide within the wreck of the SDF-1. The flowers have changed since Bowie’s last visit. Musica recognizes the blossoms at once and realizes that the Invid Flowers of Life have completed their mutation. Even now, the drifting spores are drawing the Invid to Earth across the cosmos. Bowie demands an explanation. Musica tells him: "The Invid are the enemies of both our people…The Flower of Life survives by feeding off the protoculture matrix." The young fugitives have found the factory everyone has been searching for, but it may be too late to be of any use to earth or the Robotech Masters.

Dana and crew track the couple to the ruins. They are followed in turn by Nova Satori and Zor. When confronted by the spores, Zor Prime remembers his past. He knows all of Zor’s plans and dreams. He becomes the original Zor once again.

The final offensive is underway. Alien warships move silently toward Earth. Their plan is simple – attack without retreat or surrender until they reclaim the fallen protoculture factory. General Emerson engages the enemy once again while Leonard launches his own fleet.

As the battle escalates, the Robotech Masters cast their infirm and aged citizens adrift in space. They drug their clone soldiers with anti-pain serum to enable them to fight longer. These merciless maneuvers help give them the upper hand during the brutal battle on Monument City. The Masters personally issue an ultimatum to Supreme Commander Leonard: "Evacuate the planet within thirty-eight hours or we will be forced to destroy your homeworld."

Undeterred, Commander Leonard launches a final offensive with his combined United Earth fleet and reinforcements from deep space. The Masters, anticipating Leonard's move, had secretly sends troops down to the planet to annihilate Monument City and blockade the ruins of the SDF-1. During the Masters' assault on Monument City the headquarters of the United Earth Command was vaporized, killing Leonard and many of the his senior staff that failed to evacuate. Emerson returns the battered but unbroken Southern Cross defense force to protect the planet and its people as his own flagship explodes. Marie Crystal manages to get the general into an escape pod, but they are picked up by the Robotech Masters before they can reach their own troops.

The aliens contact Zor Prime for a trade – Zor, Musica, and the dismissal of remaining Earth forces for the general and his crew. Zor accepts. As the prisoner exchange is in progress, a trap set by the Robotech Masters on their ship claims the life of Rolf Emerson. Chaos reigns as the 15th Squad desperately attempts to pull out of the area. Dana tries to relocate Zor while Sean, Marie, Bowie, and the rest of the crew look for Musica’s sisters.

Dana Sterling finds Zor determined to personally destroy the Robotech Masters. After a frantic search through the depth of the gigantic ship, Dana and Zor discover the Robotech Masters preparing a new two-front assault against the fleet and the planet. The aliens do not believe Zor wants to destroy them: "You are the embodiment of Zor, creator of the first protoculture and the Master responsible for our development. It was Zor who developed the Zentraedi people. Zor who became the prime force behind all the advancements of our society. Your most important achievement was the protoculture which brings the promise of eternal life….Surely you are not prepared to destroy your most precious creation, the embodiment of your hopes and dreams? Without it, your native civilization will wither and die."

He eliminates one of the three masters. Dana upsets the terminals that control a container of uncorrupted protoculture. She accidentally causes the seeds inside to blossom, releasing their energy. Its usefulness to the remaining Robotech Masters has been destroyed, but for Dana the energy has unleashed racial memories buried within her Zentraedi cell structure. Somehow, Dana finds the strength to reject instincts that urge her to become a part of the Robotech Masters’ culture. Hallucinations brought on by the spores leave her half-stunned.

In another section of the ship, Musica leads a battle of her own while the 15th Squad rescues civilian clones – including Musica’s sisters – marked for destruction. "I have freely chosen a new way of life!" Musica tells the Karno and his sentries. "The truth is, we are all individual beings with free will – and you know it!"

Zor Prime, having regained his memories as the original Zor, enacts his final vengeance against the Robotech Masters. Things don't exactly turn out well for anyone.

For the remained of the Robotech Masters triumvirate, the moment of retribution is at hand in the form of their rebel clone. Zor kills them. He sets Dana adrift in one of the escape modules, then prepares to destroy the ship. As he locks the controls into a crash-land position over the ruins of the SDF-1, Zor thinks to himself: "There is no other way. The destruction of this ship over the site of the battlefortress is the only guarantee that the protoculture will be obliterated before it brings the Invid to this planet!" Zor is tragically wrong. His sacrifice only compounds disaster. Instead of rendering the protoculture matrix useless, the explosion frees the mutated spores. They scatter over the planet’s surface, slowly turning Earth into a vast, fertile garden awaiting cultivation by the Invid.

The survivors of the Second Robotech War enjoy a bittersweet victory. Earth must rebuild once again – this time in the face of another potential invasion they know they cannot win.

The United Earth Forces have been broken; morale is at an all time low. Many of Earth's key military and civlian infrastructure were destroyed during the brief, but deadly war. It would take some time before the surviving members of the United Earth leadership are reorganized under a restructured command.

The Invid Invasion of Earth is swift and brutal, with many of the remaining combat units finding themselves completely overwhelmed. Earth's combined forces, weary from battle with the Robotech Masters, are no match for the battle hungry Invid, a race of protoplasmic creatures responding to the large buildup of protoculture directly attributable to the final battle of the Second Robotech War. Their supreme ruler, the Regess, has brought her entire civilization to locate and cultivate protoculture, a multipurpose energy source and food stuff, from the Flower of Life.

Thousands escape the devastated and wasted planet. Those that remain go into hiding or surrender to these new invaders. As part of the resistance and utilizing guerrilla tactics, a few Army of the Southern Cross (ASC) soldiers would continue to fight on for years to come. The Third Robotech War has begun.